On July 31, a miscommunication caused a controller at Washington's Reagan National Airport to clear two regional jets to take off toward an arriving flight.
The Inspector General's report also found evidence that more errors are occurring than the FAA has reported.
Many incidents that controllers voluntarily disclose aren't included in the agency's totals because of confidentiality rules, the report found.
The Inspector General also discovered that 157 incidents in Charlotte, N.C., weren't included in FAA totals.
In August 2011, 157 planes took off and landed on a runway at Charlotte-Douglas International Airport while a disabled commercial aircraft intruded into the runway's safety zone, according to the report.
Senior FAA officials decided not to count the incidents because they concluded that safety wasn't compromised, according to the report.
The errors that were counted in 2011 represented an increase of less than 1 percent. If the 157 incidents in Charlotte had been included, the increase would have been 9 percent.
"Until FAA takes action to determine the true magnitude of operational errors, assess their potential safety impacts, identify their root causes, and align adequate staffing for oversight, the risk of separation losses will remain a safety concern," the report said.
FAA didn't immediately respond to an e-mail request for comment. The agency agreed with at least part of all six recommendations by the Inspector General, according to the report.
The FAA plans to determine if it needs more people to investigate error reports and focus improvement efforts on the highest-risk mistakes, according to the report.